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- PDB-2vj5: Shigella flexneri MxiC -

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Basic information

Entry
Database: PDB / ID: 2vj5
TitleShigella flexneri MxiC
ComponentsPROTEIN MXIC
KeywordsTRANSPORT PROTEIN / SECRETION REGULATION / T3SS / VIRULENCE / TRANSPORT / TYPE THREE SECRETION SYSTEM
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / host cell / cell surface / extracellular region
Similarity search - Function
Arc Repressor Mutant, subunit A - #2060 / DNA polymerase; domain 1 - #630 / Monooxygenase - #240 / Salmonella/Shigella invasion protein E / : / Protein MxiC, C-terminal / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Monooxygenase ...Arc Repressor Mutant, subunit A - #2060 / DNA polymerase; domain 1 - #630 / Monooxygenase - #240 / Salmonella/Shigella invasion protein E / : / Protein MxiC, C-terminal / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Monooxygenase / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDeane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures of the Shigella Flexneri Type 3 Secretion System Protein Mxic Reveal Conformational Variability Amongst Homologues.
Authors: Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M.
History
DepositionDec 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN MXIC
B: PROTEIN MXIC


Theoretical massNumber of molelcules
Total (without water)67,2872
Polymers67,2872
Non-polymers00
Water23413
1
A: PROTEIN MXIC


Theoretical massNumber of molelcules
Total (without water)33,6431
Polymers33,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN MXIC


Theoretical massNumber of molelcules
Total (without water)33,6431
Polymers33,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.370, 91.370, 215.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.818, 0.009, 0.576), (-0.003, -1, 0.02), (0.576, -0.018, -0.818)
Vector: 11.05357, 15.08872, -35.14783)

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Components

#1: Protein PROTEIN MXIC / MXIC


Mass: 33643.301 Da / Num. of mol.: 2 / Fragment: RESIDUES 74-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HSSGLVPRGSH COMES FROM THE EXPRESSION VECTOR. THE NTERMINUS IS ABSENT FROM THE ...THE SEQUENCE HSSGLVPRGSH COMES FROM THE EXPRESSION VECTOR. THE NTERMINUS IS ABSENT FROM THE STRUCTURE, PROBABLY DUE TO PROTEOLYTIC DEGRADATION IN ABSENCE OF THE CHAPERONE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.6 %
Description: DATA INDEXED WITH LABELIT AND INTEGRATED IN XDS USING THE SUITE OF PROGRAMS XIA2
Crystal growpH: 6.5
Details: 0.2 M NA2SO4, 0.1 M BISTRISPROPANE PH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3→38.6 Å / Num. obs: 18676 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 171 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
TNT5.13.1.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VIX

2vix


Resolution: 3→38.6 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: REFINED IN BUSTER-TNT 2.1.1 WITH RESTRAINTS TO A STRUCTURE REFINED IN REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1014 5 %0.247
Rwork0.246 ---
all0.247 ---
obs0.246 17728 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 255 Å2 / ksol: 0.38 e/Å3
Refinement stepCycle: LAST / Resolution: 3→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4570 0 0 13 4583
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00592762
X-RAY DIFFRACTIONt_angle_deg0.773124642
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0032802
X-RAY DIFFRACTIONt_gen_planes0.01612965
X-RAY DIFFRACTIONt_it0.864927620
X-RAY DIFFRACTIONt_nbd0.0293915
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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